I have Wordfence scan plugin which checks our files against orignals and in some cases it seems that Super Cache and Wordfence dont work together. This note has been sent from Wordfence developer:
"We are currently aware of an issue with the “W3 total cache” and “WP Super Cache” plugins which causes Wordfence to behave erratically. In general you’ll see old status messages appearing instead of what is actually happening and you’ll see “No issues” in the security issues list when you do actually have security issues, or a list of security issues appearing when you’ve resolved everything."

Is this something you can together with Mark Maunder (developer of Wordfence) look into or is it something I can do in settings of Super Cache to avoid?